(Re)considering the Concept of Literature Review Reproducibility

Literature reviews play a key role in academic research by describing, understanding, explaining, and testing the constructs and theories within a particular topic area. In recent years, various commentaries, debates, and editorials in the information systems (IS) field’s top journals have highlighted the importance of a trustworthy literature review process, including detailed discussions on systematicity and transparency. Although the reproducibility of a literature review has also been noted as important, it remains less recognized because of several terminology-related issues. This ambiguity could result in misunderstandings regarding the degree of trust that should be placed in a literature review’s process. In this research essay, we seek to clarify what makes a literature review reproducible, how it is distinct from related concepts, and when achieving it is desirable and feasible. We propose a series of clarifications and remedies to assist scholars within and outside the IS field in the preparation of stand-alone reviews

The Gordon-Haus effect for modified NLS solitons

Random jitter in the soliton arrival time (the Gordon-Haus effect) is analyzed for solitons being solutions of the integrable modified nonlinear Schroedinger equation. It is shown that the mean square fluctuation of the soliton position depends on the soliton parameters which can be properly adjusted to suppress the Gordon-Haus jitter.Comment: LaTeX, 7 pages, 3 figures, to be published in Europhys. Let

Flavonoid Oxidation by the Radical Generator AIBN: A Unified Mechanism for Quercetin Radical Scavenging

Four oxidized flavonoid derivatives generated from reacting quercetin (a pentahydroxylated flavone) with the peroxyl radical generator 2,2′-azobis-isobutyronitrile (AIBN) were isolated by chromatographic methods and identified by NMR and MS analyses. Compounds included 2-(3,4-dihydroxybenzoyl)-2,4,6-trihydroxy-3(2H)-benzofuranone (2); 1,3,11a-trihydroxy-9-(3,5,7-trihydroxy-4H-1-benzopyran-4-on-2-yl)-5a-(3,4-dihydroxyphenyl)-5,6,11-hexahydro-5,6,11-trioxanaphthacene-12-one (3); 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoic acid (4); and methyl 3,4-dihydroxyphenylglyoxylate (5). Product ratios under different hydrogen ion concentrations and external nucleophiles revealed that two of the products, namely the substituted benzofuranone (2) and the depside (4), are generated from a common carbocation intermediate. Indirect evidence for the operation of a cyclic concerted mechanism in the formation of the dimeric produc

Stimulus - response curves of a neuronal model for noisy subthreshold oscillations and related spike generation

We investigate the stimulus-dependent tuning properties of a noisy ionic conductance model for intrinsic subthreshold oscillations in membrane potential and associated spike generation. On depolarization by an applied current, the model exhibits subthreshold oscillatory activity with occasional spike generation when oscillations reach the spike threshold. We consider how the amount of applied current, the noise intensity, variation of maximum conductance values and scaling to different temperature ranges alter the responses of the model with respect to voltage traces, interspike intervals and their statistics and the mean spike frequency curves. We demonstrate that subthreshold oscillatory neurons in the presence of noise can sensitively and also selectively be tuned by stimulus-dependent variation of model parameters.Comment: 19 pages, 7 figure

Remote sensing imagery segmentation: A hybrid approach

In remote sensing imagery, segmentation techniques fail to encounter multiple regions of interest due to challenges such as dense features, low illumination, uncertainties, and noise. Consequently, exploiting vast and redundant information makes segmentation a difficult task. Existing multilevel thresholding techniques achieve low segmentation accuracy with high temporal difficulty due to the absence of spatial information. To mitigate this issue, this paper presents a new Rényi’s entropy and modified cuckoo search-based robust automatic multi-thresholding algorithm for remote sensing image analysis. In the proposed method, the modified cuckoo search algorithm is combined with Rényi’s entropy thresholding criteria to determine optimal thresholds. In the modified cuckoo search algorithm, the Lévy flight step size was modified to improve the convergence rate. An experimental analysis was conducted to validate the proposed method, both qualitatively and quantitatively against existing metaheuristic-based thresholding methods. To do this, the performance of the proposed method was intensively examined on high-dimensional remote sensing imageries. Moreover, numerical parameter analysis is presented to compare the segmented results against the gray-level co-occurrence matrix, Otsu energy curve, minimum cross entropy, and Rényi’s entropy-based thresholding. Experiments demonstrated that the proposed approach is effective and successful in attaining accurate segmentation with low time complexity

Varieties of sawtooth behavior in TFTR plasmas

The side-viewing soft-x-ray camera on the Tokamak Fusion Test Reactor (TFTR) has made possible the observation of several different forms of sawtooth oscillation, which can be categorized according to their position in the plasma, sequence of occurrence, and patterns of associated MHD oscillation. Some insight into the plasma conditions involved can be gained by examining the waveforms in detail, along with electron temperature profiles from electron cyclotron emission measurements

Biological, clinical and population relevance of 95 loci for blood lipids.

Plasma concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with plasma lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P < 5 x 10(-8)), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes-GALNT2, PPP1R3B and TTC39B-with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD

Tokamak x ray diagnostic instrumentation

Three classes of x-ray diagnostic instruments enable measurement of a variety of tokamak physics parameters from different features of the x-ray emission spectrum. (1) The soft x-ray (1 to 50 keV) pulse-height-analysis (PHA) diagnostic measures impurity concentrations from characteristic line intensities and the continuum enhancement, and measures the electron temperature from the continuum slope. (2) The Bragg x-ray crystal spectrometer (XCS) measures the ion temperature and neutral-beam-induced toroidal rotation velocity from the Doppler broadening and wavelength shift, respectively, of spectral lines of medium-Z impurity ions. Impurity charge state distributions, precise wavelengths, and inner-shell excitation and recombination rates can also be studied. X rays are diffracted and focused by a bent crystal onto a position-sensitive detector. The spectral resolving power E/..delta..E is greater than 10/sup 4/ and time resolution is 10 ms. (3) The x-ray imaging system (XIS) measures the spatial structure of rapid fluctuations (0.1 to 100 kHZ) providing information on MHD phenomena, impurity transport rates, toroidal rotation velocity, plasma position, and the electron temperature profile. It uses an array of silicon surface-barrier diodes which view different chords of the plasma through a common slot aperture and operate in current (as opposed to counting) mode. The effectiveness of shields to protect detectors from fusion-neutron radiation effects has been studied both theoretically and experimentally

Lung eQTLs to Help Reveal the Molecular Underpinnings of Asthma

Genome-wide association studies (GWAS) have identified loci reproducibly associated with pulmonary diseases; however, the molecular mechanism underlying these associations are largely unknown. The objectives of this study were to discover genetic variants affecting gene expression in human lung tissue, to refine susceptibility loci for asthma identified in GWAS studies, and to use the genetics of gene expression and network analyses to find key molecular drivers of asthma. We performed a genome-wide search for expression quantitative trait loci (eQTL) in 1,111 human lung samples. The lung eQTL dataset was then used to inform asthma genetic studies reported in the literature. The top ranked lung eQTLs were integrated with the GWAS on asthma reported by the GABRIEL consortium to generate a Bayesian gene expression network for discovery of novel molecular pathways underpinning asthma. We detected 17,178 cis- and 593 trans- lung eQTLs, which can be used to explore the functional consequences of loci associated with lung diseases and traits. Some strong eQTLs are also asthma susceptibility loci. For example, rs3859192 on chr17q21 is robustly associated with the mRNA levels of GSDMA (P = 3.55 × 10(-151)). The genetic-gene expression network identified the SOCS3 pathway as one of the key drivers of asthma. The eQTLs and gene networks identified in this study are powerful tools for elucidating the causal mechanisms underlying pulmonary disease. This data resource offers much-needed support to pinpoint the causal genes and characterize the molecular function of gene variants associated with lung diseases

Convergent Evidence from Mouse and Human Studies Suggests the Involvement of Zinc Finger Protein 326 Gene in Antidepressant Treatment Response

OBJECTIVES: The forced swim test (FST) is a commonly used model to predict antidepressant efficacy. Uncovering the genetic basis of the model may unravel the mechanism of antidepressant treatment. METHODS: FVB/NJ (FVB) and C57BL/6J (B6) were first identified as the response and non-response strains to fluoxetine (a serotonin-specific reuptake inhibitor antidepressant) treatment in the mouse FST. Simple-interval (SIM) and composite-interval (CIM) mappings were applied to map the quantitative trait loci (QTLs) of the anti-immobility effect of fluoxetine in FST (FST(FLX)) in 865 male B6×FVB-F2 mice. The brain mRNA expressions of the gene with the maximum QTL-linkage signal for FST(FLX) after the FST were compared between B6 and FVB mice and also compared between fluoxetine and saline treatment. The association of the variants in the human homologue of the mouse FST(FLX)-QTL gene with major depressive disorder (MDD) and antidepressant response were investigated in 1080 human subjects (MDD/control = 582/498). RESULTS: One linkage signal for FST(FLX)-QTL was detected at an intronic SNP (rs6215396) of the mouse Zfp326 gene (maximal CIM-LOD = 9.36). The Zfp326 mRNA expression in the FVB thalamus was significantly down-regulated by fluoxetine in the FST, and the higher FVB-to-B6 Zfp326 mRNA expressions in the frontal cortex, striatum and hypothalamus diminished after fluoxetine treatment. Two coding-synonymous SNPs (rs2816881 and rs10922744) in the human homologue of Zfp326, ZNF326, were significantly associated with the 8-week antidepressant treatment response in the MDD patients (Bonferroni-corrected p = 0.004-0.028). CONCLUSIONS: The findings suggest the involvement of the Zfp326 and ZNF326 genes in antidepressant treatment response